1
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Liao L, Yao J, Yuan R, Xiang Y, Jiang B. Lighting-up aptamer transcriptional amplification for highly sensitive and label-free FEN1 detection. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 284:121760. [PMID: 36030671 DOI: 10.1016/j.saa.2022.121760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Specific and sensitive detection of flap endonuclease 1 (FEN1), an enzyme biomarker involved in DNA replications and several metabolic pathways, is of high values for the diagnosis of various cancers. In this work, a fluorescence strategy based on transcriptional amplification of lighting-up aptamers for label-free, low background and sensitive monitoring of FEN1 is developed. FEN1 cleaves the 5' flap of the DNA complex probe with double flaps to form a notched dsDNA, which is ligated by T4 DNA ligase to yield fully complementary dsDNA. Subsequently, T7 RNA polymerase binds the promoter region to initiate cyclic transcriptional generation of many RNA aptamers that associate with the malachite green dye to yield highly amplified fluorescence for detecting FEN1 with detection limit as low as 0.22 pM in a selective way. In addition, the method can achieve diluted serum monitoring of low concentrations of FEN1, exhibiting its potential for the diagnosis of early-stage cancers.
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Affiliation(s)
- Lei Liao
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Jianglong Yao
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Bingying Jiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China.
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2
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Jacobs RQ, Carter ZI, Lucius AL, Schneider DA. Uncovering the mechanisms of transcription elongation by eukaryotic RNA polymerases I, II, and III. iScience 2022; 25:105306. [PMID: 36304104 PMCID: PMC9593817 DOI: 10.1016/j.isci.2022.105306] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/16/2022] [Accepted: 10/03/2022] [Indexed: 11/01/2022] Open
Abstract
Eukaryotes express three nuclear RNA polymerases (Pols I, II, and III) that are essential for cell survival. Despite extensive investigation of the three Pols, significant knowledge gaps regarding their biochemical properties remain because each Pol has been evaluated independently under disparate experimental conditions and methodologies. To advance our understanding of the Pols, we employed identical in vitro transcription assays for direct comparison of their elongation rates, elongation complex (EC) stabilities, and fidelities. Pol I is the fastest, most likely to misincorporate, forms the least stable EC, and is most sensitive to alterations in reaction buffers. Pol II is the slowest of the Pols, forms the most stable EC, and negligibly misincorporated an incorrect nucleotide. The enzymatic properties of Pol III were intermediate between Pols I and II in all assays examined. These results reveal unique enzymatic characteristics of the Pols that provide new insights into their evolutionary divergence.
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Affiliation(s)
- Ruth Q. Jacobs
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Zachariah I. Carter
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aaron L. Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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3
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Fang T, Yan H, Li G, Chen W, Liu J, Jiang L. Chromatin remodeling complexes are involvesd in the regulation of ethanol production during static fermentation in budding yeast. Genomics 2019; 112:1674-1679. [PMID: 31618673 DOI: 10.1016/j.ygeno.2019.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 12/17/2022]
Abstract
The budding yeast Saccharomyces cerevisiae remains a central position among biofuel-producing organisms. However, the gene expression regulatory networks behind the ethanol fermentation is still not fully understood. Using a static fermentation model, we have examined the ethanol yields on biomass of deletion mutants for all yeast nonessential genes encoding transcription factors and their related proteins in the yeast genome. A total of 20 (about 10%) transcription factors are identified to be regulators of ethanol production during fermentation. These transcription factors are mainly involved in cell cycling, chromatin remodeling, transcription, stress response, protein synthesis and lipid synthesis. Our data provides a basis for further understanding mechanisms regulating ethanol production in budding yeast.
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Affiliation(s)
- Tianshu Fang
- Laboratory for Yeast Molecular and Cell Biology, the Research Center of Fermentation Technology, Department of Food Science, School of Agricultural Engineering and Food Sciences, Shandong University of Technology, Zibo 255000, Shandong Province, China
| | - Hongbo Yan
- Laboratory for Yeast Molecular and Cell Biology, the Research Center of Fermentation Technology, Department of Food Science, School of Agricultural Engineering and Food Sciences, Shandong University of Technology, Zibo 255000, Shandong Province, China
| | - Gaozhen Li
- Laboratory for Yeast Molecular and Cell Biology, the Research Center of Fermentation Technology, Department of Food Science, School of Agricultural Engineering and Food Sciences, Shandong University of Technology, Zibo 255000, Shandong Province, China
| | - Weipeng Chen
- Laboratory for Yeast Molecular and Cell Biology, the Research Center of Fermentation Technology, Department of Food Science, School of Agricultural Engineering and Food Sciences, Shandong University of Technology, Zibo 255000, Shandong Province, China
| | - Jian Liu
- Laboratory for Yeast Molecular and Cell Biology, the Research Center of Fermentation Technology, Department of Food Science, School of Agricultural Engineering and Food Sciences, Shandong University of Technology, Zibo 255000, Shandong Province, China
| | - Linghuo Jiang
- Laboratory for Yeast Molecular and Cell Biology, the Research Center of Fermentation Technology, Department of Food Science, School of Agricultural Engineering and Food Sciences, Shandong University of Technology, Zibo 255000, Shandong Province, China.
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4
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Herrera MC, Chymkowitch P, Robertson JM, Eriksson J, Bøe SO, Alseth I, Enserink JM. Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity. Nucleic Acids Res 2019; 46:11698-11711. [PMID: 30247619 PMCID: PMC6294503 DOI: 10.1093/nar/gky846] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/10/2018] [Indexed: 01/14/2023] Open
Abstract
tRNA genes are transcribed by RNA polymerase III (RNAPIII). During recent years it has become clear that RNAPIII activity is strictly regulated by the cell in response to environmental cues and the homeostatic status of the cell. However, the molecular mechanisms that control RNAPIII activity to regulate the amplitude of tDNA transcription in normally cycling cells are not well understood. Here, we show that tRNA levels fluctuate during the cell cycle and reveal an underlying molecular mechanism. The cyclin Clb5 recruits the cyclin dependent kinase Cdk1 to tRNA genes to boost tDNA transcription during late S phase. At tDNA genes, Cdk1 promotes the recruitment of TFIIIC, stimulates the interaction between TFIIIB and TFIIIC, and increases the dynamics of RNA polymerase III in vivo. Furthermore, we identified Bdp1 as a putative Cdk1 substrate in this process. Preventing Bdp1 phosphorylation prevented cell cycle-dependent recruitment of TFIIIC and abolished the cell cycle-dependent increase in tDNA transcription. Our findings demonstrate that under optimal growth conditions Cdk1 gates tRNA synthesis in S phase by regulating the RNAPIII machinery, revealing a direct link between the cell cycle and RNAPIII activity.
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Affiliation(s)
- Maria C Herrera
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,The Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371, Norway
| | - Pierre Chymkowitch
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway
| | - Joseph M Robertson
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jens Eriksson
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Stig Ove Bøe
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Ingrun Alseth
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jorrit M Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,The Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371, Norway
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5
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Sim J, Byun JY, Shin YB. Transcription immunoassay: light-up RNA aptamer-based immunoassay using in vitro transcription. Chem Commun (Camb) 2019; 55:3618-3621. [PMID: 30849150 DOI: 10.1039/c9cc00514e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Here, we present an ultra-enhanced immunoassay for sensitive and reliable biomarker detection using layer-by-layer assembly and transcription-assisted light-up aptamer generation to induce signal amplification. This dendrimer structure-based transcription immunoassay is ∼1500 times more sensitive than commercial fluorescence ELISA, achieving a detection limit of 108 aM.
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Affiliation(s)
- Jieun Sim
- Bionano Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.
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6
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Aptamers as Valuable Molecular Tools in Neurosciences. J Neurosci 2017; 37:2517-2523. [PMID: 28275062 DOI: 10.1523/jneurosci.1969-16.2017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/18/2017] [Accepted: 01/30/2017] [Indexed: 01/19/2023] Open
Abstract
Aptamers are short nucleic acids that interact with a variety of targets with high affinity and specificity. They have been shown to inhibit biological functions of cognate target proteins, and they are identifiable by an in vitro selection process, also termed SELEX (Systematic Evolution of Ligands by EXponential enrichment). Being nucleic acids, aptamers can be synthesized chemically or enzymatically. The latter renders RNA aptamers compatible with the cell's own transcription machinery and, thus, expressable inside cells. The synthesis of aptamers by chemical approaches opens up the possibility of producing aptamers on a large scale and enables a straightforward access to introduce modifications in a site-specific manner (e.g., fluorophores or photo-labile groups). These characteristics make aptamers broadly applicable (e.g., as an analytical, diagnostic, or separation tool). In this TechSight, we provide a brief overview on aptamer technology and the potential of aptamers as valuable research tools in neurosciences.
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7
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Inhibiting heat shock factor 1 in human cancer cells with a potent RNA aptamer. PLoS One 2014; 9:e96330. [PMID: 24800749 PMCID: PMC4011729 DOI: 10.1371/journal.pone.0096330] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 04/04/2014] [Indexed: 11/19/2022] Open
Abstract
Heat shock factor 1 (HSF1) is a master regulator that coordinates chaperone protein expression to enhance cellular survival in the face of heat stress. In cancer cells, HSF1 drives a transcriptional program distinct from heat shock to promote metastasis and cell survival. Its strong association with the malignant phenotype implies that HSF1 antagonists may have general and effective utilities in cancer therapy. For this purpose, we had identified an avid RNA aptamer for HSF1 that is portable among different model organisms. Extending our previous work in yeast and Drosophila, here we report the activity of this aptamer in human cancer cell lines. When delivered into cells using a synthetic gene and strong promoter, this aptamer was able to prevent HSF1 from binding to its DNA regulation elements. At the cellular level, expression of this aptamer induced apoptosis and abolished the colony-forming capability of cancer cells. At the molecular level, it reduced chaperones and attenuated the activation of the MAPK signaling pathway. Collectively, these data demonstrate the advantage of aptamers in drug target validation and support the hypothesis that HSF1 DNA binding activity is a potential target for controlling oncogenic transformation and neoplastic growth.
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8
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Dieci G, Bosio MC, Fermi B, Ferrari R. Transcription reinitiation by RNA polymerase III. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:331-41. [PMID: 23128323 DOI: 10.1016/j.bbagrm.2012.10.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 10/19/2012] [Accepted: 10/23/2012] [Indexed: 01/11/2023]
Abstract
The retention of transcription proteins at an actively transcribed gene contributes to maintenance of the active transcriptional state and increases the rate of subsequent transcription cycles relative to the initial cycle. This process, called transcription reinitiation, generates the abundant RNAs in living cells. The persistence of stable preinitiation intermediates on activated genes representing at least a subset of basal transcription components has long been recognized as a shared feature of RNA polymerase (Pol) I, II and III-dependent transcription in eukaryotes. Studies of the Pol III transcription machinery and its target genes in eukaryotic genomes over the last fifteen years, has uncovered multiple details on transcription reinitiation. In addition to the basal transcription factors that recruit the polymerase, Pol III itself can be retained on the same gene through multiple transcription cycles by a facilitated recycling pathway. The molecular bases for facilitated recycling are progressively being revealed with advances in structural and functional studies. At the same time, progress in our understanding of Pol III transcriptional regulation in response to different environmental cues points to the specific mechanism of Pol III reinitiation as a key target of signaling pathway regulation of cell growth. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Affiliation(s)
- Giorgio Dieci
- Dipartimento di Bioscienze, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy.
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9
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Salamanca HH, Fuda N, Shi H, Lis JT. An RNA aptamer perturbs heat shock transcription factor activity in Drosophila melanogaster. Nucleic Acids Res 2011; 39:6729-40. [PMID: 21576228 PMCID: PMC3159435 DOI: 10.1093/nar/gkr206] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Heat shock transcription factor (HSF1) is a conserved master regulator that orchestrates the protection of normal cells from stress. However, HSF1 also protects abnormal cells and is required for carcinogenesis. Here, we generate an highly specific RNA aptamer (iaRNAHSF1) that binds Drosophila HSF1 and inhibits HSF1 binding to DNA. In Drosophila animals, iaRNAHSF1 reduces normal Hsp83 levels and promotes developmental abnormalities, mimicking the spectrum of phenotypes that occur when Hsp83 activity is reduced. The HSF1 aptamer also effectively suppresses the abnormal growth phenotypes induced by constitutively active forms of the EGF receptor and Raf oncoproteins. Our results indicate that HSF1 contributes toward the morphological development of animal traits by controlling the expression of molecular chaperones under normal growth conditions. Additionally, our study demonstrates the utility of the RNA aptamer technology as a promising chemical genetic approach to investigate biological mechanisms, including cancer and for identifying effective drug targets in vivo.
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Affiliation(s)
- H Hans Salamanca
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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10
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Bi X, Guo N, Jin J, Liu J, Feng H, Shi J, Xiang H, Wu X, Dong J, Hu H, Yan S, Yu C, Wang X, Deng X, Yu L. The global gene expression profile of the model fungusSaccharomyces cerevisiaeinduced by thymol. J Appl Microbiol 2010; 108:712-22. [DOI: 10.1111/j.1365-2672.2009.04470.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Microarray analysis of p-anisaldehyde-induced transcriptome of Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2009; 37:313-22. [DOI: 10.1007/s10295-009-0676-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 11/29/2009] [Indexed: 10/20/2022]
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12
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van Werven FJ, van Teeffelen HAAM, Holstege FCP, Timmers HTM. Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome. Nat Struct Mol Biol 2009; 16:1043-8. [PMID: 19767748 DOI: 10.1038/nsmb.1674] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 08/19/2009] [Indexed: 12/13/2022]
Abstract
Transcription regulation in eukaryotes involves rapid recruitment and proper assembly of transcription factors at gene promoters. To determine the dynamics of the transcription machinery on DNA, we used a differential chromatin immunoprecipitation procedure coupled to whole-genome microarray detection in Saccharomyces cerevisiae. We find that TATA-binding protein (TBP) turnover is low at RNA polymerase I (Pol I) promoters. Whereas RNA polymerase III (Pol III) promoters represent an intermediate case, TBP turnover is high at RNA polymerase II (Pol II) promoters. Within these promoters, the highest turnover correlates with binding of the Spt-Ada-Gcn5 acetyltransferase complex (SAGA) coactivator, Mot1p dependence and presence of a canonical TATA box. In contrast, slow turnover Pol II promoters depend on TFIID and on the gene-specific factor, Rap1p. Together this shows that TBP turnover is regulated by protein factors rather than DNA sequence and argues that TBP turnover is an important determinant in regulating gene expression.
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Affiliation(s)
- Folkert J van Werven
- Department of Physiological Chemistry, University Medical Center Utrecht, Utrecht, The Netherlands
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13
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Abstract
The paradigm of gene regulation was forever changed by the discovery that short RNA duplexes could directly regulate gene expression. Most regulatory roles attributed to noncoding RNA were often repressive. Recent observations are beginning to reveal that duplex RNA molecules can stimulate gene transcription. These RNA activators employ a wide array of mechanisms to up-regulate transcription of target genes, including functioning as DNA-tethered activation domains, as coactivators and modulators of general transcriptional machinery, and as regulators of other noncoding transcripts. The discoveries over the past few years defy "Moore's law" in the breath-taking rapidity with which new roles for noncoding RNA in gene expression are being revealed. As gene regulatory networks are reconstructed to accommodate the influence of noncoding RNAs, their importance in maintenance of cellular health will become increasingly apparent. In fact, a new generation of therapeutic agents will focus on modulating the function of noncoding RNA.
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Affiliation(s)
- Aseem Z Ansari
- Department of Biochemistry & The Genome Center of Wisconsin, University of Wisconsin-Madison, 53706, USA.
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14
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Boonanuntanasarn S, Panyim S, Yoshizaki G. Characterization and organization of the U6 snRNA gene in zebrafish and usage of their promoters to express short hairpin RNA. Mar Genomics 2008; 1:115-21. [PMID: 21798162 DOI: 10.1016/j.margen.2008.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 10/23/2008] [Indexed: 10/21/2022]
Abstract
We have characterized three U6 snRNA genes in zebrafish and randomly designated them as U6-1, U6-2, and U6-3. The U6-1 gene is closely related to the mammal U6 snRNA genes and that the U6-2 and U6-3 genes are more closely related to the Drosophila and Xenopus U6 snRNA genes. The upstream regulatory sequences were located based on their conserved position relative to the transcription start site. Furthermore, we speculate that the "CCAAT box" functions as the distal sequence element in the zebrafish U6 snRNA genes. Genomic BLASTn analysis revealed that at least 555 copies of the U6-1 gene are dispersed throughout the zebrafish genome, whereas the U6-2 and U6-3 genes are each present as a single copy. Three U6 snRNA genes are functionally expressed in various tissues. All three putative promoters were able to transcribe short hairpin RNA (shRNA) in zebrafish cell extracts. Our findings demonstrate that these putative promoters have the potential to be used for vector-based RNA interference (RNAi) in zebrafish. Another U6 snRNA was found from the genomic BLASTn search and designated as U6-4, demonstrating that there are four different types of zebrafish U6 snRNA genes.
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Affiliation(s)
- Surintorn Boonanuntanasarn
- School of Animal Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Muang, Nakhon Ratchasima, 30000 Thailand
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15
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Guo N, Yu L, Meng R, Fan J, Wang D, Sun G, Deng X. Global gene expression profile ofSaccharomyces cerevisiaeinduced by dictamnine. Yeast 2008; 25:631-41. [DOI: 10.1002/yea.1614] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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16
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Shi H, Fan X, Sevilimedu A, Lis JT. RNA aptamers directed to discrete functional sites on a single protein structural domain. Proc Natl Acad Sci U S A 2007; 104:3742-6. [PMID: 17360423 PMCID: PMC1820654 DOI: 10.1073/pnas.0607805104] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Indexed: 11/18/2022] Open
Abstract
Cellular regulatory networks are organized such that many proteins have few interactions, whereas a few proteins have many. These densely connected protein "hubs" are critical for the system-wide behavior of cells, and the capability of selectively perturbing a subset of interactions at these hubs is invaluable in deciphering and manipulating regulatory mechanisms. SELEX-generated RNA aptamers are proving to be highly effective reagents for inhibiting targeted proteins, but conventional methods generate one or several aptamer clones that usually bind to a single target site most preferred by a nucleic acid ligand. We advance a generalized scheme for isolating aptamers to multiple sites on a target molecule by reducing the ability of the preferred site to select its cognate aptamer. We demonstrate the use of this scheme by generating aptamers directed to discrete functional surfaces of the yeast TATA-binding protein (TBP). Previously we selected "class 1" RNA aptamers that interfere with the TBP's binding to TATA-DNA. By masking TBP with TATA-DNA or an unamplifiable class 1 aptamer, we isolated a new aptamer class, "class 2," that can bind a TBP.DNA complex and is in competition with binding another general transcription factor, TFIIA. Moreover, we show that both of these aptamers inhibit RNA polymerase II-dependent transcription, but analysis of template-bound factors shows they do so in mechanistically distinct and unexpected ways that can be attributed to binding either the DNA or TFIIA recognition sites. These results should spur innovative approaches to modulating other highly connected regulatory proteins.
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Affiliation(s)
- Hua Shi
- *Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853; and
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222
| | - Xiaochun Fan
- *Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853; and
| | - Aarti Sevilimedu
- *Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853; and
| | - John T. Lis
- *Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853; and
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17
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Goodrich JA, Kugel JF. Non-coding-RNA regulators of RNA polymerase II transcription. Nat Rev Mol Cell Biol 2006; 7:612-6. [PMID: 16723972 DOI: 10.1038/nrm1946] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Several non-coding RNAs (ncRNAs) that regulate eukaryotic mRNA transcription have recently been discovered. Their mechanisms of action and biological roles are extremely diverse, which indicates that, so far, we have only had a glimpse of this new class of regulatory factor. Many surprises are likely to be revealed as further ncRNA transcriptional regulators are identified and characterized.
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Affiliation(s)
- James A Goodrich
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309-0215, USA.
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